Rob van Treuren

Genetic erosion in crops: concept, research results and challenges.

The loss of variation in crops due to the modernization of agriculture has been described as genetic erosion. The current paper discusses the different views that exist on the concept of genetic erosion in crops. Genetic erosion of cultivated diversity is reflected in a modernization bottleneck in the diversity levels that occurred during the history of the crop. Two stages in this bottleneck are recognized: the initial replacement of landraces by modern cultivars; and further trends in diversity as a consequence of modern breeding practices. Genetic erosion may occur at three levels of integration: crop, variety and allele. The different approaches in the recent literature to measure genetic erosion in crops are reviewed. Genetic erosion as reflected in a reduction of allelic evenness and richness appears to be the most useful definition, but has to be viewed in conjunction with events at variety level. According to the reviewed literature, the most likely scenario of diversity trends during modernization is the following: a reduction in diversity due to the replacement of landraces by modern cultivars, but no further reduction after this replacement has been completed.

Genetic diversity trends in twentieth century crop cultivars: a meta analysis

In recent years, an increasing number of papers has been published on the genetic diversity trends in crop cultivars released in the last century using a variety of molecular techniques. No clear general trends in diversity have emerged from these studies. Meta analytical techniques, using a study weight adapted for use with diversity indices, were applied to analyze these studies. In the meta analysis, 44 published papers were used, addressing diversity trends in released crop varieties in the twentieth century for eight different field crops, wheat being the most represented. The meta analysis demonstrated that overall in the long run no substantial reduction in the regional diversity of crop varieties released by plant breeders has taken place. A significant reduction of 6% in diversity in the 1960s as compared with the diversity in the 1950s was observed. Indications are that after the 1960s and 1970s breeders have been able to again increase the diversity in released varieties. Thus, a gradual narrowing of the genetic base of the varieties released by breeders could not be observed. Separate analyses for wheat and the group of other field crops and separate analyses on the basis of regions all showed similar trends in diversity.

Efficiency of reduced primer selectivity and bulked DNA analysis for the rapid detection of AFLP polymorphisms in a range of crop species

Two approaches to optimise AFLP fingerprinting forthe rapid detection of genetic polymorphisms, i.e.reduced primer selectivity and bulked DNA analysiswere examined. The efficiency of reduced primerselectivity to increase the detection frequency ofgenetic polymorphisms and to obtain more informativefingerprinting profiles was tested in six differentcrops. The number of selective nucleotides was reducedto six in onion, to five in barley, potato, lettuceand cabbage, and to four in flax. This allowed therapid identification of several primer pairs that wereable to discriminate between closely relatedgermplasm. Reproducibility tests on replicate DNAsamples indicated no major negative effects on thereliability of the fingerprinting profiles due to theuse of less selective primers, although for onionpurified DNA was needed to avoid irreproducibleresults. In barley, flax and onion, a less thanfourfold increase in the number of fragments wasobserved when primer pairs were reduced by oneselective nucleotide. This result was attributed todifferent tolerance levels for amplificationmismatches between primer pairs of differentselectivity.The efficiency of bulked DNA analysis to detectgenetic polymorphisms was investigated in differentmixtures of two barley DNA samples. AFLPs of varyingintensity could still be recovered when the two DNAswere mixed in a 1:1 ratio. However, the frequency ofrecovered bands quickly dropped when in the mixturesthe presence of the DNA carrying the fragments wasdecreased below 50%.The usefulness of the two approaches is discussed inrelation to various aspects of genetic resourcesmanagement.Two approaches to optimise AFLP fingerprinting forthe rapid detection of genetic polymorphisms, i.e.reduced primer selectivity and bulked DNA analysiswere examined. The efficiency of reduced primerselectivity to increase the detection frequency ofgenetic polymorphisms and to obtain more informativefingerprinting profiles was tested in six differentcrops. The number of selective nucleotides was reducedto six in onion, to five in barley, potato, lettuceand cabbage, and to four in flax. This allowed therapid identification of several primer pairs that wereable to discriminate between closely relatedgermplasm. Reproducibility tests on replicate DNAsamples indicated no major negative effects on thereliability of the fingerprinting profiles due to theuse of less selective primers, although for onionpurified DNA was needed to avoid irreproducibleresults. In barley, flax and onion, a less thanfourfold increase in the number of fragments wasobserved when primer pairs were reduced by oneselective nucleotide. This result was attributed todifferent tolerance levels for amplificationmismatches between primer pairs of differentselectivity.The efficiency of bulked DNA analysis to detectgenetic polymorphisms was investigated in differentmixtures of two barley DNA samples. AFLPs of varyingintensity could still be recovered when the two DNAswere mixed in a 1:1 ratio. However, the frequency ofrecovered bands quickly dropped when in the mixturesthe presence of the DNA carrying the fragments wasdecreased below 50%.The usefulness of the two approaches is discussed inrelation to various aspects of genetic resourcesmanagement.

Identification of intra-accession genetic diversity in selfing crops using AFLP markers: implications for collection management

Germplasm conserved as seeds in genebanks requires regular regeneration. In this process, selection and genetic drift may cause loss of genetic diversity from accessions. In the case of selfing crops, separation of distinct lines into different accessions may be an efficient strategy to avoid these negative effects. In order to evaluate the applicability of this method for collection management, knowledge about the level of intra-accession genetic diversity is required. By means of AFLP analysis intra-accession variation was investigated in two cultivars, two landraces and two wild populations of ex situ conserved barley germplasm. In the total sample of 216 individuals analysed (36 per accession), 22 genotypes were observed based on 104 polymorphic loci. The number of genotypes detected ranged from 1 to 3 per accession, except for a Nepalese landrace that revealed 12 genotypes. An UPGMA cluster analysis grouped the genotypes unambiguously into the accession they belonged to and genotypes within accessions were generally found to be closely related. In order to determine the repeatability of the results obtained, 11 individuals belonging to 4 genotypes from the Nepalese landrace were scored for a second set of AFLP markers. Matrices of genetic distances calculated for the two AFLP datasets were found to be highly correlated (r = 0.9346, P < 0.001). Separation of genotypes into different accessions was considered a relevant option only for the Nepalese landrace. Analysis of molecular variance indicated that this accession could be well divided into 8 distinct lines. Further implications of the results for genebank practices are discussed.Germplasm conserved as seeds in genebanks requires regular regeneration. In this process, selection and genetic drift may cause loss of genetic diversity from accessions. In the case of selfing crops, separation of distinct lines into different accessions may be an efficient strategy to avoid these negative effects. In order to evaluate the applicability of this method for collection management, knowledge about the level of intra-accession genetic diversity is required. By means of AFLP analysis intra-accession variation was investigated in two cultivars, two landraces and two wild populations of ex situ conserved barley germplasm. In the total sample of 216 individuals analysed (36 per accession), 22 genotypes were observed based on 104 polymorphic loci. The number of genotypes detected ranged from 1 to 3 per accession, except for a Nepalese landrace that revealed 12 genotypes. An UPGMA cluster analysis grouped the genotypes unambiguously into the accession they belonged to and genotypes within accessions were generally found to be closely related. In order to determine the repeatability of the results obtained, 11 individuals belonging to 4 genotypes from the Nepalese landrace were scored for a second set of AFLP markers. Matrices of genetic distances calculated for the two AFLP datasets were found to be highly correlated (r = 0.9346, P < 0.001). Separation of genotypes into different accessions was considered a relevant option only for the Nepalese landrace. Analysis of molecular variance indicated that this accession could be well divided into 8 distinct lines. Further implications of the results for genebank practices are discussed.

Spatial and temporal dynamics in genetic diversity in upland rice and late millet (Pennisetum glaucum (L.) R. Br.) in The Gambia

Ambiguity exists about the level of genetic diversity represented by farmer crop varieties, how it develops over time and how it relates to the diversity comprised by formal varieties. As part of an interdisciplinary technological/sociological study on farmer management of gene flow, upland rice (Oryza sativa L.) and late millet (Pennisetum glaucum (L.) R.Br.) from The Gambia were investigated for morphological and molecular variation. The goal of these analyses was to obtain insight into the level of crop genetic diversity of farmer’s materials planted in several case study villages in The Gambia. For both crops, samples were collected from villages and various research institutes. Based on variety names, different rice and millet varieties were expected to be used in different villages. In fact, there was a large overlap in genetic diversity for both crops, masked by the use of synonyms. The considerable similarity in rice genetic diversity between villages most likely results from the exchange of varieties between farmers. For millet this seems the result of development of varieties from the same gene pool. Some farmer varieties of rice, however, are apparent hybrid forms between the species O. sativa and O. glaberrima Steud., and farmer varieties in general displayed higher levels of genetic diversity than formal varieties. This indicates that, for rice, genetic diversity develops in farmers’ fields and may have potential use in formal breeding programs.

Reliability of germination testing of ex situ conserved seeds: a genebank case study on outsourced analyses

Germination tests are performed on a routine basis to determine the viability of genebank accessions. The results determine which accessions have to be rejuvenated. The reliability of the germination test results used by the Centre for Genetic Resources, the Netherlands was determined by the retesting of 641 random samples anonymously, in the same year and by the same testing agency as the original tests. Results showed alarmingly low reliabilities, with error levels much higher than expected based on sampling effects. The result of a germination test of a random sample with a germination of 80% was shown to have a 95% confidence interval from 63 to 97%. The errors differed strongly over crops and testing years, and were larger for crop wild relatives than for crop species.

A historical analysis of diversity trends in French and Dutch lettuce cultivars

Using historical seed catalogues in combination with molecular fingerprinting data, diversity trends of lettuce, representing an important vegetable with active breeding programmes, were studied. Seed catalogues originating from France and the Netherlands from five different decades, the earliest dating from the 1840s, were checked for the occurence of lettuce cultivars. A total of 225 catalogues, with 7,311 records of lettuce, representing 878 different cultivars were found. The number of unique cultivars on offer by French and Dutch companies showed a small continuous increase until the 1960s, after which the number of cultivars on offer more than doubled to a total of 534 in the 1990s. Only a relatively small overlap between France and the Netherlands in the range of cultivars offered was observed. The 1960s appeared to be a period with many changes: the lowest genetic diversity in lettuce cultivars was found for this decade, whereas after the 1960s the number of companies supplying lettuce seeds reduced dramatically. The percentage of companies in a decade offering an identical cultivar decreased over time, and in the 1990s almost all cultivars were unique to only a single company. The possible relations of the observed trends with the developments in plant variety protection and in the plant breeding industry are discussed.

Rapid loss of seed viability in ex situ conserved wheat and barley at 4°C as compared to −20°C storage

Wheat and barley seeds conserved for two to three decades under genebank conditions showed severe losses of viability when stored at 4°C, while no reductions were observed under −20°C. These findings should concern genebank curators, especially when suboptimal temperatures are used for long-term seed storage.